Evolution of Transmissible Gastroenteritis Virus (TGEV): A Codon Usage Perspective
Transmissible gastroenteritis virus (TGEV) is a coronavirus associated with diarrhea and high mortality in piglets. To gain insight into the evolution and adaptation of TGEV, a comprehensive analysis of phylogeny and codon usage bias was performed. The phylogenetic analyses of maximum likelihood and...
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MDPI AG
2020-10-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/21/7898 |
| _version_ | 1797549991659569152 |
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| author | Saipeng Cheng Huiguang Wu Zhenhai Chen |
| author_facet | Saipeng Cheng Huiguang Wu Zhenhai Chen |
| author_sort | Saipeng Cheng |
| collection | DOAJ |
| description | Transmissible gastroenteritis virus (TGEV) is a coronavirus associated with diarrhea and high mortality in piglets. To gain insight into the evolution and adaptation of TGEV, a comprehensive analysis of phylogeny and codon usage bias was performed. The phylogenetic analyses of maximum likelihood and Bayesian inference displayed two distinct genotypes: genotypes I and II, and genotype I was classified into subtypes Ia and Ib. The compositional properties revealed that the coding sequence contained a higher number of A/U nucleotides than G/C nucleotides, and that the synonymous codon third position was A/U-enriched. The principal component analysis based on the values of relative synonymous codon usage (RSCU) showed the genotype-specific codon usage patterns. The effective number of codons (ENC) indicated moderate codon usage bias in the TGEV genome. Dinucleotide analysis showed that CpA and UpG were over-represented and CpG was under-represented in the coding sequence of the TGEV genome. The analyses of Parity Rule 2 plot, ENC-plot, and neutrality plot displayed that natural selection was the dominant evolutionary driving force in shaping codon usage preference in genotypes Ia and II. In addition, natural selection played a major role, while mutation pressure had a minor role in driving the codon usage bias in genotype Ib. The codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses suggested that genotype I might be more adaptive to pigs than genotype II. Current findings contribute to understanding the evolution and adaptation of TGEV. |
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| id | doaj.art-c887a1ef50e0422ebe5016f3d3402e3f |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T15:22:03Z |
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| spelling | doaj.art-c887a1ef50e0422ebe5016f3d3402e3f2023-11-20T18:23:09ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-10-012121789810.3390/ijms21217898Evolution of Transmissible Gastroenteritis Virus (TGEV): A Codon Usage PerspectiveSaipeng Cheng0Huiguang Wu1Zhenhai Chen2College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, ChinaCollege of Veterinary Medicine, Yangzhou University, Yangzhou 225009, ChinaCollege of Veterinary Medicine, Yangzhou University, Yangzhou 225009, ChinaTransmissible gastroenteritis virus (TGEV) is a coronavirus associated with diarrhea and high mortality in piglets. To gain insight into the evolution and adaptation of TGEV, a comprehensive analysis of phylogeny and codon usage bias was performed. The phylogenetic analyses of maximum likelihood and Bayesian inference displayed two distinct genotypes: genotypes I and II, and genotype I was classified into subtypes Ia and Ib. The compositional properties revealed that the coding sequence contained a higher number of A/U nucleotides than G/C nucleotides, and that the synonymous codon third position was A/U-enriched. The principal component analysis based on the values of relative synonymous codon usage (RSCU) showed the genotype-specific codon usage patterns. The effective number of codons (ENC) indicated moderate codon usage bias in the TGEV genome. Dinucleotide analysis showed that CpA and UpG were over-represented and CpG was under-represented in the coding sequence of the TGEV genome. The analyses of Parity Rule 2 plot, ENC-plot, and neutrality plot displayed that natural selection was the dominant evolutionary driving force in shaping codon usage preference in genotypes Ia and II. In addition, natural selection played a major role, while mutation pressure had a minor role in driving the codon usage bias in genotype Ib. The codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses suggested that genotype I might be more adaptive to pigs than genotype II. Current findings contribute to understanding the evolution and adaptation of TGEV.https://www.mdpi.com/1422-0067/21/21/7898transmissible gastroenteritis virusphylogenycodon usage biasmutation pressureselection pressure |
| spellingShingle | Saipeng Cheng Huiguang Wu Zhenhai Chen Evolution of Transmissible Gastroenteritis Virus (TGEV): A Codon Usage Perspective International Journal of Molecular Sciences transmissible gastroenteritis virus phylogeny codon usage bias mutation pressure selection pressure |
| title | Evolution of Transmissible Gastroenteritis Virus (TGEV): A Codon Usage Perspective |
| title_full | Evolution of Transmissible Gastroenteritis Virus (TGEV): A Codon Usage Perspective |
| title_fullStr | Evolution of Transmissible Gastroenteritis Virus (TGEV): A Codon Usage Perspective |
| title_full_unstemmed | Evolution of Transmissible Gastroenteritis Virus (TGEV): A Codon Usage Perspective |
| title_short | Evolution of Transmissible Gastroenteritis Virus (TGEV): A Codon Usage Perspective |
| title_sort | evolution of transmissible gastroenteritis virus tgev a codon usage perspective |
| topic | transmissible gastroenteritis virus phylogeny codon usage bias mutation pressure selection pressure |
| url | https://www.mdpi.com/1422-0067/21/21/7898 |
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